LibSBML tutorials

Here we provide access to a number of presentations that deal with particular aspects of using libSBML together with same sample coding exercises (with answers). These are adapted versions of tutorials given in the past.

Presentations

• Building and installing – This tutorial shows how to build and install libSBML.
• Getting started with programming – This tutorial gives a very basic introduction to the libSBML API. It focusses on how the API relates to SBML components and attributes.
• Using MIRIAM annotations – This tutorial provides information on the custom API included within libSBML that facilitates the use of MIRIAM compliant annotations.
• Using MATLAB/Octave – This tutorial gives a brief introduction to building, installing and using the libSBML interface to either MATLAB and Octave.
• L3 Package extensions – This tutorial deals with how to develop the plugin code that allows an SBML Level 3 package to be included with libSBML-5. It deals purely with the libSBML extension classes that register an extension and shows how to include an additional element and also an additional attrbute with a core element.

Exercises

1. Read in Model_1.xml and produce the list of reaction equations contained in the model. (i.e. information of the form: Reaction 1: A + B -> C; where A,B,C reflect the ‘name’ of the species - not the ‘id’).

• Sample code
• Sample C++ code
• Sample Java code

2. Create a model which encodes the following: Four parameters, p1, p2, p3 and p4, where

   p2 = 3*p1
   p3 = p1*p2
   d(p4)/dt = p3/time
   p1 = x metres
   x is some unknown number
   

You will need to look at InitialAssignments/AssignmentRules/RateRules/csymbol time. To make it slightly harder, try to fully specify the units for each parameter.

• Sample code
• Sample C++ code
• Sample Java code
• Sample model